Nowadays, oil companies employ nanofluid flooding to increase oil production from oil reservoirs. Herein the present work, a multiphase flow in porous media was used to simulate oil extraction from a three-dimensional porous medium filled with oil. Interestingly, the finite element method was used to solve the nonlinear partial differential equations of continuity, energy, Darcy’s law, and the transport of nanoparticles (NPs). The proposed model used nanofluids (NFs) empirical formulas for density and viscosity on NF and oil relative permeabilities and NP transport equations. The NPs thermophysical properties have been investigated and compared with their oil recovery factor (ORF) to determine the highest ORF. Different NPs (SiO2, CuO, and Al2O3) were used as the first parameter, keeping all parameters constant. The simulation was run three times for the injected fluid using the various NPs to compare the effects on enhanced oil recovery. The second parameter, volume fraction (VF), has been modeled six times (0.5, 1, 2, 3, 4, and 5%), with all other parameters held constant. The third parameter, the injected NF inlet temperature (293.15–403.15 K), was simulated assuming that all other parameters are kept constant. The energy equation was applied to choose the inlet temperature that fits the optimum NP and VF to determine the highest ORF. Findings indicated that SiO2 shows the best ORF compared to the other NPs. Remarkably, SiO2 has the lowest density and highest thermal capacity. The optimum VF of SiO2 was 4%, increasing the ORF but reduced when the VF was higher than 4%. The ORF was improved when the viscosity and density of the oil decreased by increasing the injected inlet temperature. Furthermore, the results indicated that the highest ORF of 37% was obtained at 353.15 K when SiO2 was used at a VF of 4%. At the same time, the lowest recovery is obtained when a volume of 5% was used at 403.15 K.